Rsubread 1.9.3
Wei Shi
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsubread | | Last Changed Rev: 74594 / Revision: 74774 | | Last Changed Date: 2013-03-19 20:53:18 -0700 (Tue, 19 Mar 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | [ OK ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rsubread.buildbin-libdir Rsubread_1.9.3.tar.gz'
>>>>>>>
* installing *source* package 'Rsubread' ...
@@@@@ The operation system is supposed to be Darwin.
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c R_wrapper.c -o R_wrapper.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c SNPCalling.c -o SNPCalling.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c aligner.c -o aligner.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c atgcContent.c -o atgcContent.o
atgcContent.c: In function 'retrieve_sequence':
atgcContent.c:54: warning: unused variable 'data_ready'
atgcContent.c:52: warning: unused variable 'offset'
atgcContent.c:51: warning: unused variable 'readlen'
atgcContent.c:49: warning: unused variable 'z'
atgcContent.c:48: warning: unused variable 'len'
atgcContent.c: In function 'atgcContent':
atgcContent.c:90: warning: unused variable 'z'
atgcContent.c:89: warning: unused variable 'len'
atgcContent.c:92: warning: 'readlen' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c detectionCall.c -o detectionCall.o
detectionCall.c: In function 'build_ir_data_structure_map':
detectionCall.c:156: warning: unused variable 'read_entrezid'
detectionCall.c: In function 'simplify_SAM_file':
detectionCall.c:194: warning: unused variable 'z'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c detectionCallAnnotation.c -o detectionCallAnnotation.o
detectionCallAnnotation.c: In function 'build_ir_data_structure':
detectionCallAnnotation.c:96: warning: unused variable 'read_length'
detectionCallAnnotation.c: In function 'breakIntegenicRegion':
detectionCallAnnotation.c:131: warning: unused variable 'read_length'
detectionCallAnnotation.c:131: warning: unused variable 'read_entrezid'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c exon-algorithms.c -o exon-algorithms.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c exon-align.c -o exon-align.o
exon-align.c: In function 'get_grouped_position':
exon-align.c:786: warning: pointer of type 'void *' used in arithmetic
exon-align.c:786: warning: pointer of type 'void *' used in subtraction
exon-align.c:793: warning: pointer of type 'void *' used in arithmetic
exon-align.c:793: warning: pointer of type 'void *' used in arithmetic
exon-align.c: In function 'junction_tree_b_explorer':
exon-align.c:835: warning: pointer of type 'void *' used in arithmetic
exon-align.c:835: warning: pointer of type 'void *' used in arithmetic
exon-align.c:835: warning: pointer of type 'void *' used in subtraction
exon-align.c:853: warning: pointer of type 'void *' used in arithmetic
exon-align.c: In function 'junction_tree_f_explorer':
exon-align.c:975: warning: pointer of type 'void *' used in arithmetic
exon-align.c:975: warning: pointer of type 'void *' used in arithmetic
exon-align.c:975: warning: pointer of type 'void *' used in subtraction
exon-align.c:999: warning: pointer of type 'void *' used in arithmetic
exon-align.c: In function 'merge_pos_table':
exon-align.c:1644: warning: pointer of type 'void *' used in subtraction
exon-align.c:1646: warning: pointer of type 'void *' used in arithmetic
exon-align.c:1647: warning: pointer of type 'void *' used in arithmetic
exon-align.c:1647: warning: pointer of type 'void *' used in arithmetic
exon-align.c: In function 'merge_connection_table':
exon-align.c:1668: warning: pointer of type 'void *' used in subtraction
exon-align.c:1670: warning: pointer of type 'void *' used in arithmetic
exon-align.c:1706: warning: pointer of type 'void *' used in arithmetic
exon-align.c: In function 'remove_neighbours':
exon-align.c:1810: warning: pointer of type 'void *' used in arithmetic
exon-align.c:1830: warning: pointer of type 'void *' used in arithmetic
exon-align.c:1831: warning: pointer of type 'void *' used in arithmetic
exon-align.c: In function 'put_connection_table':
exon-align.c:1984: warning: pointer of type 'void *' used in arithmetic
exon-align.c:1990: warning: pointer of type 'void *' used in arithmetic
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c fullscan.c -o fullscan.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c gene-algorithms.c -o gene-algorithms.o
gene-algorithms.c: In function 'find_and_explain_indel':
gene-algorithms.c:917: warning: overflow in implicit constant conversion
gene-algorithms.c: In function 'explain_indel_in_middle':
gene-algorithms.c:1068: warning: overflow in implicit constant conversion
gene-algorithms.c:1095: warning: overflow in implicit constant conversion
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c gene-value-index.c -o gene-value-index.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c hashtable.c -o hashtable.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c index-builder.c -o index-builder.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c input-files.c -o input-files.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c processExons.c -o processExons.o
processExons.c: In function 'find_chr':
processExons.c:216: warning: unused variable 'pt'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c propmapped.c -o propmapped.o
propmapped.c: In function 'propmapped':
propmapped.c:21: warning: unused variable 'z'
propmapped.c:20: warning: unused variable 'len'
propmapped.c:49: warning: control reaches end of non-void function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c qualityScores.c -o qualityScores.o
qualityScores.c: In function 'retrieve_scores':
qualityScores.c:17: warning: unused variable 'data_ready'
qualityScores.c:12: warning: unused variable 'z'
qualityScores.c:11: warning: unused variable 'len'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c readSummary.c -o readSummary.o
readSummary.c: In function 'readSummary':
readSummary.c:116: warning: suggest explicit braces to avoid ambiguous 'else'
readSummary.c:193: warning: format '%d' expects type 'int', but argument 5 has type 'long int'
readSummary.c:193: warning: format '%d' expects type 'int', but argument 6 has type 'long int'
readSummary.c:26: warning: unused variable 'z'
readSummary.c:25: warning: unused variable 'len'
readSummary.c:205: warning: control reaches end of non-void function
readSummary.c:18: warning: 'read_length' may be used uninitialized in this function
readSummary.c:44: warning: 'fragment_length' may be used uninitialized in this function
readSummary.c:44: warning: 'mate_pos' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c removeDupReads.c -o removeDupReads.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c sam2bed.c -o sam2bed.o
sam2bed.c: In function 'sam2bed':
sam2bed.c:23: warning: unused variable 'z'
sam2bed.c:22: warning: unused variable 'len'
sam2bed.c:52: warning: control reaches end of non-void function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c sorted-hashtable.c -o sorted-hashtable.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Rsubread.so R_wrapper.o SNPCalling.o aligner.o atgcContent.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align.o fullscan.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-files.o processExons.o propmapped.o qualityScores.o readSummary.o removeDupReads.o sam2bed.o sorted-hashtable.o -lpthread -DMAKE_FOR_EXON -D MACOS -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/Rsubread.buildbin-libdir/Rsubread/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'Rsubread.Rnw'
** testing if installed package can be loaded
* DONE (Rsubread)
>>>>>>>
>>>>>>> FIXING LINKS FOR Rsubread.buildbin-libdir/Rsubread/libs/i386/Rsubread.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "Rsubread.buildbin-libdir/Rsubread/libs/i386/Rsubread.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "Rsubread.buildbin-libdir/Rsubread/libs/i386/Rsubread.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "Rsubread.buildbin-libdir/Rsubread/libs/i386/Rsubread.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "Rsubread.buildbin-libdir/Rsubread/libs/i386/Rsubread.so"
>>>>>>>
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=Rsubread.buildbin-libdir --libs-only Rsubread_1.9.3.tar.gz'
>>>>>>>
* installing *source* package 'Rsubread' ...
@@@@@ The operation system is supposed to be Darwin.
** libs
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c R_wrapper.c -o R_wrapper.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c SNPCalling.c -o SNPCalling.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c aligner.c -o aligner.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c atgcContent.c -o atgcContent.o
atgcContent.c: In function 'retrieve_sequence':
atgcContent.c:54: warning: unused variable 'data_ready'
atgcContent.c:52: warning: unused variable 'offset'
atgcContent.c:51: warning: unused variable 'readlen'
atgcContent.c:49: warning: unused variable 'z'
atgcContent.c:48: warning: unused variable 'len'
atgcContent.c: In function 'atgcContent':
atgcContent.c:90: warning: unused variable 'z'
atgcContent.c:89: warning: unused variable 'len'
atgcContent.c:92: warning: 'readlen' may be used uninitialized in this function
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c detectionCall.c -o detectionCall.o
detectionCall.c: In function 'build_ir_data_structure_map':
detectionCall.c:156: warning: unused variable 'read_entrezid'
detectionCall.c: In function 'simplify_SAM_file':
detectionCall.c:194: warning: unused variable 'z'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c detectionCallAnnotation.c -o detectionCallAnnotation.o
detectionCallAnnotation.c: In function 'build_ir_data_structure':
detectionCallAnnotation.c:96: warning: unused variable 'read_length'
detectionCallAnnotation.c: In function 'breakIntegenicRegion':
detectionCallAnnotation.c:131: warning: unused variable 'read_length'
detectionCallAnnotation.c:131: warning: unused variable 'read_entrezid'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c exon-algorithms.c -o exon-algorithms.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c exon-align.c -o exon-align.o
exon-align.c: In function 'get_grouped_position':
exon-align.c:786: warning: pointer of type 'void *' used in arithmetic
exon-align.c:786: warning: pointer of type 'void *' used in subtraction
exon-align.c:793: warning: pointer of type 'void *' used in arithmetic
exon-align.c:793: warning: pointer of type 'void *' used in arithmetic
exon-align.c: In function 'junction_tree_b_explorer':
exon-align.c:835: warning: pointer of type 'void *' used in arithmetic
exon-align.c:835: warning: pointer of type 'void *' used in arithmetic
exon-align.c:835: warning: pointer of type 'void *' used in subtraction
exon-align.c:853: warning: pointer of type 'void *' used in arithmetic
exon-align.c: In function 'junction_tree_f_explorer':
exon-align.c:975: warning: pointer of type 'void *' used in arithmetic
exon-align.c:975: warning: pointer of type 'void *' used in arithmetic
exon-align.c:975: warning: pointer of type 'void *' used in subtraction
exon-align.c:999: warning: pointer of type 'void *' used in arithmetic
exon-align.c: In function 'merge_pos_table':
exon-align.c:1644: warning: pointer of type 'void *' used in subtraction
exon-align.c:1646: warning: pointer of type 'void *' used in arithmetic
exon-align.c:1647: warning: pointer of type 'void *' used in arithmetic
exon-align.c:1647: warning: pointer of type 'void *' used in arithmetic
exon-align.c: In function 'merge_connection_table':
exon-align.c:1668: warning: pointer of type 'void *' used in subtraction
exon-align.c:1670: warning: pointer of type 'void *' used in arithmetic
exon-align.c:1706: warning: pointer of type 'void *' used in arithmetic
exon-align.c: In function 'remove_neighbours':
exon-align.c:1810: warning: pointer of type 'void *' used in arithmetic
exon-align.c:1830: warning: pointer of type 'void *' used in arithmetic
exon-align.c:1831: warning: pointer of type 'void *' used in arithmetic
exon-align.c: In function 'put_connection_table':
exon-align.c:1984: warning: pointer of type 'void *' used in arithmetic
exon-align.c:1990: warning: pointer of type 'void *' used in arithmetic
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c fullscan.c -o fullscan.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c gene-algorithms.c -o gene-algorithms.o
gene-algorithms.c: In function 'find_and_explain_indel':
gene-algorithms.c:917: warning: overflow in implicit constant conversion
gene-algorithms.c: In function 'explain_indel_in_middle':
gene-algorithms.c:1068: warning: overflow in implicit constant conversion
gene-algorithms.c:1095: warning: overflow in implicit constant conversion
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c gene-value-index.c -o gene-value-index.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c hashtable.c -o hashtable.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c index-builder.c -o index-builder.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c input-files.c -o input-files.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c processExons.c -o processExons.o
processExons.c: In function 'find_chr':
processExons.c:216: warning: unused variable 'pt'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c propmapped.c -o propmapped.o
propmapped.c: In function 'propmapped':
propmapped.c:21: warning: unused variable 'z'
propmapped.c:20: warning: unused variable 'len'
propmapped.c:49: warning: control reaches end of non-void function
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c qualityScores.c -o qualityScores.o
qualityScores.c: In function 'retrieve_scores':
qualityScores.c:17: warning: unused variable 'data_ready'
qualityScores.c:12: warning: unused variable 'z'
qualityScores.c:11: warning: unused variable 'len'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c readSummary.c -o readSummary.o
readSummary.c: In function 'readSummary':
readSummary.c:116: warning: suggest explicit braces to avoid ambiguous 'else'
readSummary.c:193: warning: format '%d' expects type 'int', but argument 5 has type 'long int'
readSummary.c:193: warning: format '%d' expects type 'int', but argument 6 has type 'long int'
readSummary.c:26: warning: unused variable 'z'
readSummary.c:25: warning: unused variable 'len'
readSummary.c:205: warning: control reaches end of non-void function
readSummary.c:18: warning: 'read_length' may be used uninitialized in this function
readSummary.c:44: warning: 'fragment_length' may be used uninitialized in this function
readSummary.c:44: warning: 'mate_pos' may be used uninitialized in this function
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c removeDupReads.c -o removeDupReads.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c sam2bed.c -o sam2bed.o
sam2bed.c: In function 'sam2bed':
sam2bed.c:23: warning: unused variable 'z'
sam2bed.c:22: warning: unused variable 'len'
sam2bed.c:52: warning: control reaches end of non-void function
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c sorted-hashtable.c -o sorted-hashtable.o
gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Rsubread.so R_wrapper.o SNPCalling.o aligner.o atgcContent.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align.o fullscan.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-files.o processExons.o propmapped.o qualityScores.o readSummary.o removeDupReads.o sam2bed.o sorted-hashtable.o -lpthread -DMAKE_FOR_EXON -D MACOS -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/Rsubread.buildbin-libdir/Rsubread/libs/x86_64
* DONE (Rsubread)
>>>>>>>
>>>>>>> FIXING LINKS FOR Rsubread.buildbin-libdir/Rsubread/libs/x86_64/Rsubread.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "Rsubread.buildbin-libdir/Rsubread/libs/x86_64/Rsubread.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "Rsubread.buildbin-libdir/Rsubread/libs/x86_64/Rsubread.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "Rsubread.buildbin-libdir/Rsubread/libs/x86_64/Rsubread.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "Rsubread.buildbin-libdir/Rsubread/libs/x86_64/Rsubread.so"